


A Light in the Shadows

by just_one_more_nerd



Category: Shadowhunters (TV)
Genre: Alternate Universe - Canon Divergence, Character Death, Eventual Magnus Bane/Alec Lightwood, I Wrote This Instead of Sleeping, Kid Fic, Slow Burn, Tags May Change, at the beginning, but it happens before the story starts, they grow up
Language: English
Status: In-Progress
Published: 2020-07-16
Updated: 2020-08-25
Packaged: 2021-03-04 19:55:15
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 2
Words: 2,666
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/25301941
Author URL: https://archiveofourown.org/users/just_one_more_nerd/pseuds/just_one_more_nerd
Summary: Jocelyn killed Valentine during The Uprising before fleeing with the cup and Luke, about thirteen years later the few former circle members who had managed to escape the clave found out where she was hiding. Jocelyn, Luke, and Dot all died in the attack but managed to take out all the circle members and the demons they had hired. Clary was found in her bedroom clutching a stele, the last thing her mother had given her before making her hide in her room.OR: What if Magnus raised Clary?(currently rewriting what I have so far)
Relationships: Alec Lightwood & Isabelle Lightwood & Jace Wayland, Clary Fray & Simon Lewis, Clary Fray/Jace Wayland, Magnus Bane & Clary Fray, Magnus Bane/Alec Lightwood
Comments: 6
Kudos: 51





	1. Chapter 1

For the first time since the worst night of her life Clary was going back to her childhood home. For the last month she’d been staying with Simon’s family. They said she was welcome to stay as long as she had to, but Clary saw the relief in Mrs. Lewis’s face when she heard that the will was going to be read early because it was going to be used in the decision of who got custody of Clary. Clary knew that Simon’s family had all been going through a lot since his dad died, and even though she was terrified at the thought of ending up with some stranger, the last thing she wanted to do was make things harder for her best friend and his family, especially after they’d done so much for her.

Mrs. Lewis was holding her as they walked through the store. Since that night someone had cleaned up a bit. Looking at the missing windows covered in paper, Clary remembered the broken glass. She saw the place where they kept the antique goblets was totally decemated. Most of them were missing, and the ones that weren’t were broken. 

Mrs. Lewis squeezed her hand, and Clary finally moved forward, walking through the shop and into her home. Looking around she remembered peeking out of her bedroom and seeing her mother using a glowing sword to fight monsters and other people with glowing swords. She hadn’t seen Luke, but she did see a giant wolf attacking one of the glowy sword people, and how there had been light coming out of Dot’s hands. She’d tried to tell the police officer about what she’d seen, but he didn’t believe her. After that she didn’t tell anyone, she was scared they’d think she was crazy. 

When they got to the dining room, Clary sat down at the table with Mrs. Lewis. The only other person there was a man with a briefcase sitting at the head of the table. He had a sheet of paper in front of him, and he was clearly waiting for something. They all sat there for a few minutes before a man with glittery makeup and gravity defying hair walked in and sat down at the table across from Clary.

“I’m sorry ma'am, but you can’t be here” the lawyer said to Mrs. Lewis, she gave Clary a hug before leaving through the store. “The will’s very straight forward so I’ll just read out what Jocelyn wrote, I leave everything to my dearest Clary, I love you more than words can say. Should I die before Clary’s Eighteenth birthday Luke Garoway and Dorothea Rollins will get custody of Clary, and if they died at the same time as me, Magnus Bane will get custody of Clary. That’s it,” the lawyer said, and if that surprised the glittery man, Magnus, she assumed, he didn’t show it. The lawyer handed Magnus a letter with his name on it and started packing up his things. Clary thought it was a little weird that her mother anticipated that her, Dot, and Luke would all die at the same time, but she didn’t think about it then.

Being back in this place so soon was too much for her. After the stress of the will reading was gone, what this all really meant started crashing down on her. Her mom, Dot, and Luke were all gone forever, there had been monsters, real monsters, she didn’t care if no one believed her, and now she had to go live with a stranger. It was all so much, and suddenly she couldn’t really breath right, when a soft and calming voice cut through her stress.

“Hey Biscuit,” Magnus said suddenly on her side of the table, and in the seat next to her so he was at her eye level. “try and breath with me ok?” and Clary nodded quickly. “In, and out, in, and out.” he said, repeating it until Clary’s breathing was back to normal. “Let’s get you home.”

Clearly wasn’t sure what it was, but there was just something that felt so familiar about Magnus, it was like there were memories that she couldn’t reach. She leaned in and gave him a hug. He was clearly surprised, but after a moment he hugged her back. 

By this time the lawyer was gone. “Ok, can you hold my hand and close your eyes? I promise I’ll explain everything after you’ve gotten a good night’s sleep,” Magnus said. Clary grabbed his hand very tight, and closed her eyes. She heard something that sounded like swirling air, and then suddenly it felt like she was being twisted and spun in the middle of the air, until her feet hit the ground again. “Ok, you can open your eyes” now Magnus said.

She was standing in front of a pair of black doors with metal lines across them. “How is that-” Clary started before being cut off by Magnus.

“I promise I’ll explain everything in the morning,” he said, “welcome home Clary.” He pushed the doors open and Clary stepped into her new home.

\---

(the next day)

Clary woke up, and for a split second she didn’t recognise the room, but then everything came flooding back to her. The will, Magnus, and suddenly appearing at his house. She got out of bed and walked into the living room in her PJs, cozy fleece pants and a sweater she’d stolen from her mom. In the living room she found breakfast laid out, and Magnus sitting at one of the two place settings scrolling through his phone. 

He looked up as Clary sat down, “good, you're awake, you’ll want to eat before we talk.” After they ate, they walked over to the couch. “Your mother told me that if anything should ever happen to her that I was to tell you everything, so here goes.” Magnus says, taking a deep breath, “everything you saw that night was real, the monsters, the glowing swords, and Dorothea’s magic. All the legends are true, there are vampires, werewolves, like Luke, seelie, or the fair folk, and finally there are Warlocks, like me and Dorothea. We make up the downworld, we have demon blood, and it gives us power, but we are not demons. That’s not to say that demons aren’t real, they are, they’re the monsters you saw that night. 

“There is also one more type of people that aren’t mundane, that’s what we call normal people, the shadowhunters. Your parents were shadowhunters, and by blood you are too. Shadowhunters are people with angel blood who are trained from a young age to fight demons and keep the world safe from them. The people with glowing swords were shadowhunters who defected and believed that not just demons, but anyone with demon blood, like me, Dorothea, and Luke, should die. Your mother stopped their plan to kill a lot of innocent people, and they wanted revenge, that’s why they came after you.”

“How did I not know about this,” asked Clary.

“Oh, but you did Biscuit,” Magnus said with a fond smile. “You should know that everything your mother did, she did to protect you, she wanted to be able to live a mundane life for as long as possible. Shadowhunters are trained from birth to be soldiers, weapons for The Clave, that’s the shadowhunter government, to move as they please. That’s the reason she left your care to me instead of them, and also the reason she had me take all your memories of the shadow world.”

“You whAT?” asked Clary, suddenly standing up.

“No need to panic, now that you know about the shadow world, I’ll of course return them to you, that was always the plan. Since Valentine, the leader of the evil shadowhunters, is gone, there was no reason for me to hide them.” Magnus said.

“Yeah, I think that’d be good.” said Clary, sitting back down.

“Ok, this may sting a bit.” said Magnus pulling a blue string of light from his temple. He shifted it between his hands and turned it into a ball of light before pressing it against Clary’s forehead. Suddenly Clary’s head was being filled with new memories. A demon attacking her at the park. Finding the hiding spot of the glowing sword, a seraph blade she now remembered hearing Luke call it, and it lighting up when she touched it. Her hands tied to a chair and Magnus tried to talk her mom out of doing this, her insisting, and him taking the memories. 

Suddenly they were all gone, finding their places amongst the rest of her memories, and all she could feel was a pounding headache. “Oh, dear” she heard Magnus say, but it sounded far away. She saw him raise his hands near her head and started waving them around. Another blue light appeared, and suddenly the headache was gone, replaced by a calming cool sensation. 

When Magnus was done healing her, and the blue light of his magic was gone, Clary leaned forward and hugged him. Magnus was surprised by the sudden show of affection, but hugged her back anyway. “Why?” he asked “you just found out that I took your memories, how can you forgive me so easily?”

“You just gave me back moments with my mother that I didn’t even know I was missing. On top of that, you took me in when you didn’t have to, you saved me from becoming a soldier.” said Clary.

“Oh Biscuit, of course I did. You’re twelve, you should be thinking about seventh grade, not fighting demons.” Magnus said. He pulled away from the hug, but left his hands on Clary’s shoulders and looked into her eyes as he said. “However, this world is a dangerous one, and just being aware of it puts you at risk, that’s why your mother went to such extremes to keep it from you. So while I refuse to have you throw your life away to become a puppet for the Clave, you must learn to defend yourself.” 

“That’s fair.” Clary said, “but I’ll still be able to go to school and hang out with Simon, right?”

“Of course,” Magnus reassured her, “I’ll do everything in my power to give the mundane life that your mother wanted for you.”


	2. Chapter 2

(6 years later)

Jace was chasing a drevak demon through the streets. Moments like this, on the hunt with Alec and Izzy, running through the streets with his seraph blade in hand were what he lived for. He rounded the corner into an ally where he saw the demon had a young woman with red hair cornered. He was about to leap into action, but before he had time to move the girl had pulled out dual kindjal blades and cut down the monster herself. 

The demon disintegrated which meant that the blades had been made adamus, and the glowing inscriptions meant she had angel blood, but before he could get a good look at them the girl glamoured them away. By this point Izzy and Alec had caught up to him. “I chased it around here, and it was about to attack that girl when she pulled out dual kindjals and sent it back to Edom herself,” Jace explained.

“She’s a shadowhunter?” asked Izzy. “Then why have none of us met her? And where are all her runes?”

“She could have gone rogue or maybe even be part of a new version of The Circle, either way we have to bring her in to be questioned.” said Alec.

“Oh come on Alec, all she did was defend herself,” said Izzy.

“Alec’s right,” said Jace. Izzy and Alec were both surprised for a moment before realising it probably had more to do with needing an excuse to talk to a pretty girl than following Clave protocol. Jace quickly walked up to the red head, “Hi, I’m Jace” he said, “and these are my siblings Alec and Izzy. We’re the top shadowhunters at the New York Institute. You should come back there with us, it is you know, one of the top institutes world wide, and a great place to go for a talented nephilim like you, looking for a new institute to call home.”

“What Jace means to say,” said Alec, “is that since you’re not registered to the NY institute, and you’re on the hunt in our territory, we have to bring you in for some routine questions.”

“I’m Clary,” the girl said. “First off, I wasn’t on the hunt, I was minding my own business when that demon attacked me, it was self defence. Second, I may be a shadowhunter by blood, but I’m an artist at heart, and as lovely as being forced back to your institute and interrogated sounds, I have an early morning tomorrow and my dad will be worried sick if I’m not home soon, so if you don’t mind,”

“Sorry, but you should really come with up” Alec interrupted, not sounding very sorry at all. “If you don’t come willingly we’ll be forced to arrest you.”

“Ok then, lead the way,” Clary said, frustration clear in her voice. “But you should really let me call my dad first, let him know I’m not dead.”

“Sorry, we can’t do that,” said Izzy, who unlike her brother really did seem sorry. “It’s too likely you’ll call some to break you out.”

\---

After they arrived at the institute and we’re settled in a room, Clary asked to call her dad again. “Look, it’s really in your best interest to let me call him,” she explained. “If I don’t call him he’ll freak out and track me here, and if he thinks I’m in danger who knows how many people he’ll hurt to get to me.” 

Alec couldn’t help but roll his eyes, “don’t worry about us, this is a heavily guarded building filled with fully trained shadowhunters.” 

“Oh, the wards won’t be a problem” Clary said, thinking back to the time that Magnus had told her about how he had put up those wards himself over a hundred years ago, and even though his technique had greatly improved since then the institute had never asked him to update them. 

“Ok, back to the questions,” said Alec. “What’s your full name? Why do none of us know you? How did you get adamus blades if your not an official shadowhunter?” Alec was clearly just getting started, but he was interrupted by a loud bang. 

“I told you that you should have let me call him” Clary said with a smirk. The door was kicked down and a man wearing an intricate silk shirt, unbuttoned most of the way, a couple necklaces, and glittery make-up entered the room. Alec knew he should do something, but his breath caught in his throat and he froze. 

“Biscuit!” the man yelled, running over to Clary and giving her a hug, “if they touched a hair on your head I swear to-”

“I’m fine, but can we get out of here? I’ve had a really long day,” Clary said.

“Of course” the man said, before opening a portal in the middle of the institute, Alec didn’t even know that was possible. The two strangers walked through the portal unhindered, as the siblings were all too confused to react. 

“Do either of you know what just happened?” asked Jace. 

“I need both of you to figure out who this mystery not quite shadowhunter girl is, and why she referred to a warlock as her father, I’ll reach out to the nearest high warlock, our wards clearly need an update. Also, keep this between the three of us, there may be a perfectly reasonable explanation for this and there’s no reason for us to bring to clave into this and potentially ruin this girl’s life. Are we clear?” Alec got a nod from both his siblings before leaving the room to go do research on the High Warlock of Brooklyn.

**Notes for the Chapter:**

> the plan is to make this a series, this first story with my original plot idea, the second with oneshots set during clary's childhood, and the third an epilogue or sequel, idk yet. no beta, all the mistakes are mine. all comments and kudos are really appreciated. thanks for reading :)

**Author's Note:**

> Yes, I am aware that this isn't how custody or will readings work, just please ignore that, thanks! I really appreciate all feedback and comments, it's been a really long time since I've written, and this is my first time writing in this fandom. Also yes, this will eventually become Malec, but it might take a while.
> 
> I know the title sucks but I have no idea what to call this. If you have any ideas, pleeease put them in the comments. :)


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